Variant report

Variant	rs37238
Chromosome Location	chr5:89824976-89824977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	UBTF	chr5:89824326-89826236	K562	blood:	n/a	n/a
2	ZEB1	chr5:89824743-89825678	GM12878	blood:	n/a	chr5:89825161-89825170 chr5:89825258-89825270 chr5:89825162-89825173
3	TCF12	chr5:89824687-89826218	A549	lung:	n/a	chr5:89825149-89825159
4	ZNF143	chr5:89824771-89826429	K562	blood:	n/a	n/a
5	POLR2A	chr5:89824308-89826235	K562	blood:	n/a	n/a
6	EGR1	chr5:89824768-89825761	K562	blood:	n/a	chr5:89825152-89825162 chr5:89825463-89825477 chr5:89825373-89825384 chr5:89825543-89825552 chr5:89825216-89825226 chr5:89825372-89825385 chr5:89825479-89825493 chr5:89825478-89825491 chr5:89825152-89825165
7	EGR1	chr5:89824874-89825748	K562	blood:	n/a	chr5:89825152-89825162 chr5:89825463-89825477 chr5:89825373-89825384 chr5:89825543-89825552 chr5:89825216-89825226 chr5:89825372-89825385 chr5:89825479-89825493 chr5:89825478-89825491 chr5:89825152-89825165
8	POLR2A	chr5:89824932-89825458	GM12878	blood:	n/a	n/a
9	CEBPB	chr5:89824300-89826211	Hela-S3	cervix:	n/a	n/a
10	TCF7L2	chr5:89824647-89826132	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr5:89824923-89826359	K562	blood:	n/a	n/a
12	RFX5	chr5:89824952-89826099	HepG2	liver:	n/a	n/a
13	CTCF	chr5:89824880-89826659	SK-N-SH	brain:	n/a	chr5:89825024-89825032
14	YY1	chr5:89824907-89825635	HepG2	liver:	n/a	chr5:89825374-89825383 chr5:89825251-89825273 chr5:89825294-89825306 chr5:89825478-89825489 chr5:89825417-89825426
15	MAX	chr5:89824802-89826148	K562	blood:	n/a	n/a
16	POLR2A	chr5:89824811-89826159	H1-neurons	neurons:	n/a	n/a
17	IRF1	chr5:89824705-89826239	K562	blood:	n/a	chr5:89824857-89824871 chr5:89826042-89826051
18	POLR2A	chr5:89824317-89826185	GM12878	blood:	n/a	n/a
19	POLR2A	chr5:89824567-89826134	K562	blood:	n/a	n/a
20	MAFK	chr5:89824825-89825078	HepG2	liver:	n/a	chr5:89824870-89824887
21	TAF1	chr5:89824965-89826079	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr5:89821851-89826472	K562	blood:	n/a	n/a
23	RFX5	chr5:89824759-89826402	Hela-S3	cervix:	n/a	n/a
24	YY1	chr5:89824831-89825027	K562	blood:	n/a	n/a
25	SIN3AK20	chr5:89824821-89825578	K562	blood:	n/a	n/a
26	POLR2A	chr5:89824732-89826153	Raji	blood:	n/a	n/a
27	EP300	chr5:89824639-89826652	K562	blood:	n/a	chr5:89826147-89826156 chr5:89825539-89825555
28	MAX	chr5:89824954-89826266	A549	lung:	n/a	chr5:89826147-89826156
29	POLR2A	chr5:89824937-89826062	ProgFib	skin:	n/a	n/a
30	BCLAF1	chr5:89824942-89825599	GM12878	blood:	n/a	chr5:89825478-89825487
31	ELK4	chr5:89824917-89825588	Hela-S3	cervix:	n/a	n/a
32	MAX	chr5:89824963-89825634	MCF-7	breast:	n/a	n/a
33	MAZ	chr5:89824971-89826286	GM12878	blood:	n/a	chr5:89826147-89826156
34	SIN3A	chr5:89824870-89826086	GM12878	blood:	n/a	n/a
35	POLR2A	chr5:89824228-89826067	HepG2	liver:	n/a	n/a
36	YY1	chr5:89824968-89826117	GM12892	blood:	n/a	chr5:89825374-89825383 chr5:89825251-89825273 chr5:89825294-89825306 chr5:89825478-89825489 chr5:89825417-89825426 chr5:89825908-89825917
37	SIN3AK20	chr5:89824882-89825674	PANC-1	pancreas:	n/a	n/a
38	HMGN3	chr5:89824817-89826053	K562	blood:	n/a	n/a
39	ZC3H11A	chr5:89824872-89826217	K562	blood:	n/a	n/a
40	STAT5A	chr5:89824786-89825455	GM12878	blood:	n/a	n/a
41	SIN3AK20	chr5:89824780-89825497	H1-hESC	embryonic stem cell:	n/a	n/a
42	E2F4	chr5:89824971-89825908	K562	blood:	n/a	chr5:89825543-89825552
43	YY1	chr5:89824905-89825693	K562	blood:	n/a	chr5:89825374-89825383 chr5:89825251-89825273 chr5:89825294-89825306 chr5:89825478-89825489 chr5:89825417-89825426
44	MXI1	chr5:89824574-89826192	HepG2	liver:	n/a	n/a
45	RCOR1	chr5:89824569-89826214	Hela-S3	cervix:	n/a	n/a
46	EP300	chr5:89824970-89826268	GM12878	blood:	n/a	chr5:89826147-89826156 chr5:89825539-89825555
47	CCNT2	chr5:89824329-89826030	K562	blood:	n/a	chr5:89825477-89825486
48	REST	chr5:89824760-89826356	H1-neurons	neurons:	n/a	chr5:89825143-89825156
49	YY1	chr5:89824584-89826113	GM12878	blood:	n/a	chr5:89825374-89825383 chr5:89825251-89825273 chr5:89825294-89825306 chr5:89825478-89825489 chr5:89825417-89825426 chr5:89825908-89825917
50	POLR2A	chr5:89824955-89825560	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:89703358..89707086-chr5:89823955..89827154,6	MCF-7	breast:
2	chr5:89823137..89824981-chr5:89966228..89967935,2	K562	blood:
3	chr5:89766469..89774126-chr5:89823341..89829105,11	K562	blood:
4	chr5:89822684..89827061-chr5:89851623..89857043,7	MCF-7	breast:
5	chr5:89705290..89707109-chr5:89824364..89826854,3	MCF-7	breast:
6	chr5:89704960..89708059-chr5:89823269..89827144,6	K562	blood:
7	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
8	chr5:89768691..89773005-chr5:89822332..89827140,9	MCF-7	breast:
9	chr5:89703407..89707223-chr5:89822965..89826833,10	K562	blood:
10	chr5:89767818..89772796-chr5:89823286..89827702,11	MCF-7	breast:

Variant related genes	Relation type
GPR98	TF binding region
ENSG00000164199	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000255647	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10069050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154568	0.89[EUR][1000 genomes]
rs154569	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs154570	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs154572	0.84[EUR][1000 genomes]
rs154573	0.85[EUR][1000 genomes]
rs1553545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171790	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs250377	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs257850	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257851	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2656957	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27198	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs27201	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs37239	0.83[EUR][1000 genomes]
rs37240	0.83[EUR][1000 genomes]
rs42467	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs43149	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs491082	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511393	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs526806	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs556894	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59159252	0.84[ASN][1000 genomes]
rs594990	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs599432	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs625135	0.92[CEU][hapmap]
rs679568	0.96[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884154	0.81[EUR][1000 genomes]
rs790081	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs810974	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs37238	GPR98	cis	cerebellum	SCAN
rs37238	GPR98	cis	parietal	SCAN
rs37238	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL
rs37238	LYSMD3	cis	normal skin	skin_eQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89822600-89826600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr5:89823000-89825000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:89823200-89825000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:89823200-89826200	Active TSS	Right Atrium	heart
5	chr5:89823200-89826200	Active TSS	NHLF	lung
6	chr5:89823400-89825000	Flanking Active TSS	Dnd41	blood
7	chr5:89823400-89826400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:89823600-89825000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr5:89823600-89825000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr5:89823600-89825200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:89823600-89826000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:89823600-89826200	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr5:89823600-89826200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:89823600-89826200	Active TSS	Fetal Intestine Large	intestine
15	chr5:89823600-89826200	Active TSS	K562	blood
16	chr5:89823600-89826200	Active TSS	NH-A	brain
17	chr5:89823600-89826200	Active TSS	NHDF-Ad	bronchial
18	chr5:89823600-89826400	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr5:89823600-89826400	Active TSS	GM12878-XiMat	blood
20	chr5:89823800-89825200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:89823800-89826200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr5:89823800-89826200	Active TSS	HMEC	breast
23	chr5:89823800-89826400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:89824000-89825000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:89824000-89825200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr5:89824000-89826000	Active TSS	NHEK	skin
27	chr5:89824000-89826200	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr5:89824000-89826200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:89824000-89826200	Active TSS	Colonic Mucosa	Colon
30	chr5:89824000-89826200	Active TSS	Colon Smooth Muscle	Colon
31	chr5:89824000-89826200	Active TSS	Right Ventricle	heart
32	chr5:89824000-89826400	Active TSS	H1 Cell Line	embryonic stem cell
33	chr5:89824000-89826400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:89824000-89826600	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr5:89824000-89826600	Active TSS	Aorta	Aorta
36	chr5:89824000-89826600	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr5:89824000-89826600	Active TSS	HSMMtube	muscle
38	chr5:89824200-89825000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:89824200-89825000	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr5:89824200-89825000	Flanking Active TSS	Fetal Brain Male	brain
41	chr5:89824200-89825200	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr5:89824200-89825200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr5:89824200-89825200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr5:89824200-89825200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr5:89824200-89826000	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr5:89824200-89826000	Active TSS	Placenta	Placenta
47	chr5:89824200-89826000	Active TSS	Placenta Amnion	Placenta Amnion
48	chr5:89824200-89826200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:89824200-89826200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:89824200-89826200	Active TSS	Brain Angular Gyrus	brain

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